The route was initially designed to run the full distance between Minneapolis and Rice, Minnesota, near St. Cloud. Because of the high costs, that plan was not well received by Minnesota politicians. More importantly since the project was counting on federal funding for half of its construction costs, the projected ridership for the full route was not high enough to qualify for that much needed federal funding[citation needed]. Governor Jesse Ventura was an early advocate of the Northstar commuter rail line and convinced some people to come around to his point of view.[6] However, former Governor Tim Pawlenty did not initially support the idea and said he would not support it when he campaigned for the governorship. He changed his mind after the Federal Transit Administration determined that a scaled-back version of the line would cost less to initially build and would have lower maintenance costs after going into operation than the original plan.

Many hoped that funds would be approved for the project during Minnesota's 2004 legislative session, but the representatives at the capitol were unable to find common ground on a number of issues, the issuing of bonds among them. The project appeared stalled and many requested the governor to call a special session of the legislature, but some counties in the area and the Metropolitan Council came up with matching funds to allow funding from the United States federal government to continue.

During the 2005 legislative session, a bonding bill very similar to the proposed 2004 bonding bill was passed, including $37.5 million of funding for the corridor. The issue was believed to have changed the composition of the Minnesota House as the election in 2004 saw at least two non-supporters in direct vicinity of the Corridor ousted by opposition candidates. The bill was signed on April 11, 2005, by Governor Tim Pawlenty at the site of the Riverdale station in Coon Rapids, Minnesota.[7] This funding along with a total of $55 million in local funding was matched with Federal funds and allowed the NCDA to enter Final Design. A nearly $1 billion budget bill passed by the legislature in May 2006 provided funding to complete the corridor to Big Lake.[8]

Construction began on the maintenance facility near Big Lake station and on the Blue Line light rail extension in September 2007, before full funding for the line had been secured.[5] On December 11, 2007, U.S. Deputy Secretary of Transportation Thomas Barrett met with Governor Pawlenty in Anoka County and officially signed a Full Funding Grant Agreement of $156.8 million, nearly half of the funding for the $317 million, 40-mile (64 km) line from Minneapolis to Big Lake. The money enabled the release of an additional $97.5 million in state bonding money set aside for the project.[9][10]

The federal government paid $156.8 million, the state paid $98.6 million and the Anoka County Regional Rail Authority pledged $34.8 million. The remaining partners were Sherburne County Regional Rail Authority ($8.2 million), Hennepin County Regional Rail Authority ($8 million), the Metropolitan Council ($5.9 million) and the Minnesota Twins ($2.6 million, for the station improvements under the new Target Field where the Minneapolis station was constructed).[9] $107.5 million of the $317 million total went to paying BNSF for a perpetual easement for track rights and facilities along the line and to pay the BNSF employees that operate the trains. Another significant chunk of the cost went into the Blue Line light rail extension. The operating budget for the first full year of service, 2010, was $16.8 million.[11]

The Minnesota Department of Transportation (Mn/DOT) and the Northstar Corridor Development Authority (NCDA) studied options for development of the corridor to handle the increasing commuter load and felt that a commuter rail line was the best option. It was expected to cost about US$265 million in 2008 dollars, estimated to be less than one-third the cost of upgrading existing highways,[12][13] though the cost would later climb to $317 million.[11] Because most of the rail that is being used already exists, the costs mostly went into building new train stations, upgrading track, enhancing crossings, and updating signals. A significant portion of the cost was used in extending the METROBlue Line to the Target Field station on the west side of Interstate 394 and 5th Street. This terminal station is integrated into the Minnesota Twins' new ballpark, Target Field, which opened in March 2010.

Bus feeder lines, including the Northstar Link from St. Cloud to Big Lake station,[14] bring residents who live along the corridor to the nearest train station. Once in downtown Minneapolis, commuters can walk upstairs to the METRO Blue and Green Lines, take a bus into other neighboring areas, or go into one of the nearby buildings integrated into the Minneapolis skyway system. The line currently has six trains running in the morning and evening rush hour periods, and limited service on weekends and holidays. Metro Ridership in 2010 fell well short of its goal of 3,400 weekday trips. Metro Transit has a goal for of 5,900 by 2030.[15] saving those commuters 900,000 hours over the course of a year when compared to taking a dedicated bus line.[12]

Ridership in the first 15 days averaged 2,207 per day (33,112 total), short of a goal of 2,460.[17] By the end of January 2010, goals were exceeded by 3%.[18] Ridership for 2010 was originally projected to be 897,000 though ultimately ended up at 715,000.[19] Because ridership varies significantly through the course of a year, Metro Transit's month-to-month goals are different than the yearly average goal.

The route travels north through the Northtown Classification Yards, over Interstate 694 and makes its first stop at 61st Avenue in Fridley at the yard limit of Northtown, where it enters BNSF's Staples Subdivision. The double track line continues past the current Foley Boulevard park-and-ride bus station, which is planned to be a future Northstar station and turns northwest at Coon Creek Junction, where the old GN route to Duluth (now BNSF's Hinckley Subdivision) splits off and heads straight north. The current Coon Rapids station is behind the Riverdale shopping center by Round Lake Boulevard and new stations were also built in Anoka, Elk River, and Big Lake.

The Great Northern Railway and Northern Pacific Railway had local services from Minneapolis to all of the cities currently served by Northstar up through the early 20th century. One Fridley station was about a mile north of the current stop, at Mississippi Boulevard. There possibly was a stop shared by GN and NP at Coon Creek Junction.[20] There were at least three stations built in Anoka over the years, while there were each two stations in Elk River and Big Lake, with both cities having one stop for each railroad.[21]

The double-track main line between Northtown Yard in Minneapolis and Coon Creek Junction in Coon Rapids is the busiest rail corridor in the Twin Cities metropolitan area. In July 2009, before the Northstar Commuter Rail commuter line began operation, this segment had hosted 63 trains per day.[22] The Minnesota Department of Transportation would like to run more passenger trains through the corridor, including Northstar and other proposed passenger rail routes like the proposed Northern Lights Express to Duluth. A $113.4 million project to add a third main line and a new station at Foley Boulevard in Coon Rapids is planned. A $99 million grant request was filed under the American Recovery and Reinvestment Act of 2009 to cover most of the cost.[23] TIGER grants are expected to be awarded on February 17, 2010.[24]

Foley station was among cuts to the Northstar plan in 2003 while federal funding was being sought prior to construction. Despite the fact the 3,200-stall parking facility already existed (sans boarding platforms), riders would not save enough time by switching from existing bus service to rail to make the stop fit within the guidelines enforced by Federal Transit Administration's cost-effectiveness index.[25] A station in Ramsey at Ramsey Town Center was also cut prior to construction. Ramsey station construction has been fully funded, and construction began on March 27, 2012[26] and was completed on November 8.[27] The station was opened on November 14, 2012.[28]

A major obstacle to extending Northstar to St. Cloud is the lack of double-tracked rail for nine miles (14 km) from Big Lake to Becker.[29] The Minnesota Department of Transportation says that extending Northstar would result in 1 to 1.5 million annual trips on the line[citation needed]. In its 2010 State Rail Plan, the agency stated an expectation of farebox recovery ratios between 70% and 111% on the full line.[30] However, the same plan had estimated farebox recovery ratios of just 21% to 34% on the proposed Northern Lights Express, which had calculated ratios of over 100% in a 2007 business plan.[31]

On November 8, 2010, it was announced that the planned extension of the line to St. Cloud had been indefinitely delayed. Projected ridership is not sufficient to qualify for federal funding.[32]

Northstar operates on one of the busiest freight rail corridors in Minnesota with up to fifty freight trains per day plus the twice daily Amtrak Empire Builder. Freight traffic has increased in recent years due to the oil boom in North Dakota, with BNSF hauling the crude oil from North Dakota through the Twin Cities. This has caused severe delays for the Empire Builder and Northstar. Another cause of delays were the extremely low temperatures during the winter of 2013, which affected the speed trains could go, how long railroad crews could work outside, the locomotives, and signaling and switches.

Since the summer of 2014, BNSF has done maintenance on the tracks used by Northstar in order to increase efficiency and reduce delays for trains. Maintenance work will resume October 20 and work will be finished by the start of winter. While there will be delays for commuter trains up to 20 minutes when maintenance work resumes, Metro Transit has stated that the track work will ensure the reliability of Northstar and eliminate delays.

The line opened in 2009 with five MP36PH-3C locomotives and seventeen Bombardier BiLevel Coach cars. Each passenger car has about 140 seats and room for 355 when full with standees. The coaches have two doors on either side.[33] Upon the opening, Metro Transit immediately announced that a sixth locomotive was being acquired from the Utah Transit Authority's FrontRunner service in the Salt Lake City area and a lease agreement was soon signed.[17] Typical weekday operation requires five trains, each consisting of one locomotive and three or four coaches. A single train is used for weekend service, making three round trips each day. The platforms are only designed for five-car trains, so longer trains would require additional construction.

Metro Transit did begin experimenting in April 2010 with six-car trains for taking riders to and from weekend Twins games at Target Field.[34] These trains overhang the platform at either end and only open one door on each of the end cars. In May, trains serving Twins games grew to eight cars, with some completely overhanging the platforms so some riders would have to board and then walk from one car to another.[35] By June, Metro Transit had decided to purchase the sixth locomotive it had leased from UTA due to high leasing costs and the need to have an extra locomotive for when others are being repaired or inspected. $2.85 million for buying the locomotive and repainting it in Northstar livery came from a $10.1 million contingency fund built into the original cost of the service.[36]

By October 2014, there had been at least 4 deaths involving Northstar trains, with the latest being in Elk River on October 22. There have also been 2 train vs. car crashes. In October 2014, a trainset was vandalized at the maintenance facility in Big Lake, bringing the total number of incidents on the line to 7.